Data from: A new plant virus discovered by immunocapture of double stranded RNA; assessment of a novel approach for viral metagenomics studies

Next-generation sequencing technologies enable the rapid identification of viral infection of diseased organisms. However, despite a consistent decrease in sequencing costs, it is difficult to justify their use in large-scale surveys without a virus sequence enrichment technique. As the majority of plant viruses have an RNA genome, a common approach is to extract the double-stranded RNA (dsRNA) replicative form, to enrich the replicating virus genetic material over the host background. The traditional dsRNA extraction is time-consuming and labour-intensive. We present an alternative method to enrich dsRNA from plant extracts using anti-dsRNA monoclonal antibodies in a pull-down assay. The extracted dsRNA can be amplified by reverse transcriptase–polymerase chain reaction and sequenced by next-generation sequencing. In our study, we have selected three distinct plant hosts: Māori potato (Solanum tuberosum), rengarenga (Arthropodium cirratum) and broadleaved dock (Rumex obtusifolius) representing a cultivated crop, a New Zealand-native ornamental plant and a weed, respectively. Of the sequence data obtained, 31–74% of the reads were of viral origin, and we identified five viruses including Potato virus Y and Potato virus S in potato; Turnip mosaic virus in rengarenga (a new host record); and in the dock sample Cherry leaf roll virus and a novel virus belonging to the genus Macluravirus. We believe that this new assay represents a significant opportunity to upscale virus ecology studies from environmental, primary industry and/or medical samples.

下一代测序技术（Next-generation sequencing）可快速鉴定染病生物的病毒感染情况。然而，尽管测序成本持续下降，但若缺乏病毒序列富集技术，仍难以证明其在大规模调查中的应用合理性。由于大多数植物病毒的基因组为RNA，常用方法是提取双链RNA（double-stranded RNA, dsRNA）复制型，以在宿主背景中富集复制中的病毒遗传物质。传统dsRNA提取方法耗时费力。本研究提出一种替代方案：利用抗dsRNA单克隆抗体进行下拉实验，从植物提取物中富集dsRNA。提取得到的dsRNA可通过逆转录聚合酶链式反应（reverse transcriptase-polymerase chain reaction, RT-PCR）进行扩增，再通过下一代测序技术完成测序。本研究选取了三种不同的植物宿主：分别为毛利马铃薯（Solanum tuberosum）、龙舌兰百合（Arthropodium cirratum，俗称rengarenga）以及宽叶酸模（Rumex obtusifolius，俗称broadleaved dock），对应栽培作物、新西兰本土观赏植物与杂草三类样本。在所获得的测序数据中，31%~74%的读段来自病毒序列；我们共鉴定出5种病毒：马铃薯样本中检出马铃薯Y病毒（Potato virus Y）与马铃薯S病毒（Potato virus S）；龙舌兰百合样本中检出芜菁花叶病毒（Turnip mosaic virus），此为该宿主的新记录；宽叶酸模样本中检出樱桃卷叶病毒（Cherry leaf roll virus）以及一种隶属于马卢拉病毒属（Macluravirus）的新型病毒。我们认为，该新型检测方法为从环境、第一产业及/或医学样本中开展病毒生态学研究提供了重要的规模化机遇。